[Chimera-users] Question related to chimera H-bond constraints

[Elaine Meng]

Dear S,
In both #1 and #2 you have checked "Relax" so you are using the  
relaxed values, and will get the same total (76).  The only difference  
is coloring: in #1 all 76 are colored cyan, whereas in #2 the ones  
meeting the strict criteria (50) are cyan and the ones that do not  
meet the strict criteria but do meet the relaxed criteria (26) are  
red.  In #3 you only have the strict ones.
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 24, 2010, at 10:21 AM, snoze pa wrote:

> Dear Chimera Users,
>
> I have a question related to number of hydrogen bonds.
>
> 1.  When I am using the Relax H-bond constraints then chimera is
> showing 76 H-bonds as shown below figure (h bonds are shown in cyan
> color)
>
> http://img260.imageshack.us/img260/6467/screenshotau.png
>
> 2. If I will select the option color H bonds not meeting precise
> criteria differently, then still it shows 76 H bonds with some bonds
> that do not meet the criteria in red color
>
> http://img690.imageshack.us/img690/5607/screenshot1ks.png
>
> In 2, Why the red H bonds are different from 1 though H bonds are
> relaxed. If it is true then why chimera is showing these bonds in
> Relax H-bond constraints in 1.
>
> 3. However, if I will not choose the option to relax H bonds
> constraints then it is showing 50 H bonds as shown below
>
> http://img153.imageshack.us/img153/3822/screenshot2kr.png
>
> Thank you very much for your time and help.
>
> S
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